User: Floor Stam

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Floor Stam90
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14 years, 11 months ago
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15 years, 10 months ago
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f*****@bio.vu.nl

Posts by Floor Stam

<prev • 9 results • page 1 of 1 • next >
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clustering & memory
... hi there I am using R1.9.1 under mac OSX on an Apple iBook 640MB ram I'm trying to cluster my genes, and run into a memory problem (or at least, that's what it looks like). When i do: >single.clust<-function(d) hclust(d, method="single") >eucl.dist <- function(x) dist(x, method="euc ...
clustering written 15.0 years ago by Floor Stam90 • updated 15.0 years ago by Jenny Bryan110
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Comment: C: GoStats
... hi michael In case you're impatient: i wrote a function (it's at the bottom of this message) that sort of does what you want automatically. I need to warn you beforehand: i am a biologist and a beginner at R so it's not perfect at all! The table you get as an output will need some cleaning up as yo ...
written 15.1 years ago by Floor Stam90
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Answer: A: AnnBuilder/ABPkgBuilder: lots of Errors
... I'm running R 1.9.1 on mac OSX using AnnBuilder 1.4.2. When i try to build an annotation package using AnnBuilder i get an error using the following code: > myDir<-("/Data_analyse") > myBase<-file.path("GBbase.txt") > myBaseType<-"gb" ShowmyBase<-read.table("GBbase.txt") S ...
written 15.2 years ago by Floor Stam90
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AnnBuilder/ABPkgBuilder: lots of Errors
... Hi I'd like to build an Annotation package for the (custom made rat) array that i'm using. I'm running R 1.9.1 on mac osx and have an installation failure of AnnBuilder 1.4.13 I installed the devel versions of biobase and annotate as well, xml 0.95-6 is also installed. install.from.file(pkg="/Use ...
annotation go cancer organism biobase annotate annbuilder process bridge written 15.2 years ago by Floor Stam90 • updated 15.2 years ago by John Zhang2.9k
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Answer: A: Correct use of a distance measure when clustering gene expression data
... Hi Mick I think it depends on the kind of similarity that is important to you. -If you think it is important that genes that show parallel profiles are clustered together, use pearsons correlation coefficient. In this case two genes that peak at the same moment in time, but at a (very) different h ...
written 15.2 years ago by Floor Stam90
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Answer: A: human tissue specific genes
... You can use NCBI's library browser and 'digital differential expression': http://www.ncbi.nlm.nih.gov/UniGene/info_ddd.html Floor Stam On 2 Aug 2004 , at 7:17, Lana Schaffer wrote: > Greetings, > I am wondering if someone knows a source of obtaining a list of the > human tissue > s ...
written 15.3 years ago by Floor Stam90
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Answer: A: maNorm 2D
... Hi Matthew tRMA (http://www.cmis.csiro.au/iap/tRMA/docs/tRMA.pdf) also has a spatial-normalisation function, this one is described in a paper by Wilson et al. in Bioinformatics (june 2003). It is better documented and, in fact, the only one that worked for me since the 2Dloess function in the maNor ...
written 15.5 years ago by Floor Stam90
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Answer: A: recipe for installing and using Bioconductor with Mac OS X 10.3 and R GUI 1.9
... ...and make sure you have the Xtools installed. Affy and some other packages like xml do not install without them. floor > Dear Colleagues -- > > I've been trying unsuccessfully to use Bioconductor (mostly the affy > package) on a Mac with OS X 10.3.3, running R with a GUI, either 1.8 ...
written 15.6 years ago by Floor Stam90
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Installing Bioconductor on MAC
... I think panther is 10.3, isn't it? It is running fine on my iBook, but i don't use, and therefore never tried, affy. Sometimes it works better to download the packages manually and install them from the folder (or .zip) on your desktop, or download and install the source. I have noticed that there ...
cancer affy written 15.9 years ago by Floor Stam90

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